Changes in kaiA, an important clock gene in cyanobacteria

The BLAST search of the GenBank database also returned several short proteins manifesting high homology to other segments of the KaiA domain. For example, the proteins from two cyanobacterial strains annotated as Cyanobacteria bacterium QH_1_48_107 and Cyanobacteria bacterium QS_7_48_42, possess the KaiA homologs of 56 residues long (PSO52447.1↗ and PSP04869.1↗, respectively), which match a region between positions 169 and 224 in the bona fide S. elongatus PCC7942 protein (hereinafter the position numbers refer to the bona fide KaiA sequence). Interestingly, both these strains possess KaiC but lack KaiB.

Another example is the KaiA homologs found in some Prochlorococci (Table S1). They vary from 62 to 66 residues in length and, unlike the previous ones, match residues 238–284 in the respective S. elongatus PCC7942 protein (Fig. 1e). In contrast to the above-mentioned two strains, Prochlorococci do possess both KaiB and KaiC.

Several strains of Prochlorococcus sp. (e.g., MIT9303, MIT9313, and MIT1306) possessed a gene located in the genomic region usually occupied by the kaiA gene in the syntenic bona fide kaiABC operon, i.e. between the rplU and kaiB genes. However, unlike kaiA, this gene is located on the reverse complement strand. This gene was previously described as a pseudogene in MIT9303 and MIT9313¹². However, this is apparently not so: according to the genomic annotations, the gene is apparently translated, because it contains an open reading frame and thus may be functional. The putative respective proteins were about the same length (65–132 aa) as the sdKaiA homologs in other cyanobacteria. However, these proteins showed no apparent homology to either KaiA or any other proteins in the non-redundant NCBI protein database according to the BLAST search. Their function remains unknown.

In addition to cyanobacteria, the KaiA protein was found in other marine and freshwater bacteria, e.g., Propionibacteriaceae bacterium and Planctomycetaceae bacterium TMED241 (Table S1). This finding is unlikely an artefact, because screening of this species’ genome assembly revealed the full syntenic kaiABC operon typically found in cyanobacteria.

According to the Conserved Domain Database¹³, the N-terminal domain of the bona fide ddKaiA protein of S. elongatus PCC7942 belongs to the OmpR family. However, the observed homology is quite weak and was detected only when a lower E-value was applied. OmpR is a DNA-binding dual transcriptional regulator and is often an element of various two-component regulatory systems. While most ddKaiA proteins share the above architecture, few of them manifest some variability by featuring other domains instead of OmpR, namely REC, AtoC or PHA02030↗ (Fig. 1). However, regardless of the domain architecture, all KaiA homologs appear to form a homodimer in solution^14,15. On the other hand, this may not be the case for the truncated homologs.

The kaiA genes in some species are annotated as pseudogenes as, for example, in Aphanizomenon ovalisporum (CDHJ01000032↗, locus tag apha_00336). The functional deficiency of their KaiA might result by lack of the N-terminal fragment.

The analysis of the functional divergence between the single-domain and double-domain KaiA proteins showed the significantly altered functional constraints (rates of evolution) after duplication of the ancestral gene. On the other hand, no type II functional divergence (radical amino acid changes without a rate shift) was detected. In the analyzed segment of 96 amino acid residues (nearly the full length KaiA domain), the effective number of the type I residues was 33. That means, nearly 1/3 of the domain experienced significant shift in evolutionary rate.

The C-terminal region of ddkaiA is more variable (d_N = 0.30 ± 0.03, π = 0.36 ± 0.00) as compared to the single-domain homologs (d_N = 0.20 ± 0.02, π = 0.26 ± 0.01) and is much more conserved than the N-terminal one (d_N = 0.88 ± 0.06, π = 0.52 ± 0.00). This may be due to the evolutionary younger age of sdKaiAs as compared to ddKaiAs (Nostocales are evolutionary younger than Oscillatoriophycideae, Synechococcales and Pleurocapsales)¹⁰ or/and because of the higher functional significance of the C-terminal region of KaiA (binds to KaiB and KaiC)²⁰. Besides, the N-terminal domains of the ddkaiA genes may vary and manifest functional diversity (Fig. 1). None of the applied methods detected positive selection in the kaiA genes.

The time estimates of the major events in the evolution of the kaiA homologs are provided in Table 3. Both Bayesian and ML estimates are similar and suggest three main periods when these events probably occurred: about 30–100, 500–600, and 1000–1500 Mya. The origin of the sdkaiA was apparently associated with the origin of Chroococcidiopsidales that occurred about 1500 Mya.

The kaiA genes were found in all analyzed cyanobacteria except Gloeobacter. The latter is thought to be the most ancient cyanobacterium, which, while being able for photosynthesis, lacks a few structures and genes common for all other cyanobacteria²¹. Our results on the kaiA occurrence are essentially in agreement with those recently reported by Schmelling et al.²² who performed comprehensive screening of prokaryotes for circadian orthologs. In addition, the present study firstly reports the kaiA homologs and the whole kaiABC operon in prokaryotes other than cyanobacteria. The most probable explanation of this may be a lateral transfer of the operon from cyanobacteria.

The truncated kaiA homologs from Prochlorococcales were not reported by the early evolutionary studies of the circadian system in cyanobacteria (see, e.g.^10,11). This might be due to the much smaller volume of then available genomic data and poor annotations of genomes.

The occurrence of the kaiA homologs across all cyanobacterial taxa suggests that this gene is of ancient origin, probably as old as most cyanobacteria themselves. Indeed, kaiA was found in the thermophilic strains from Yellowstone, Synechococcus sp. JA-2-3B'a(2-13) and Synechococcus sp. JA-3-3Ab, which are located at the root of the cyanobacterial phylogenetic subtree (Figs. 3a and S1a). It might be that the gene was horizontally transferred from the evolutionary younger lineages. However, no such transfers to this clade was detected (Fig. S2).

In the pioneering study about origin and evolution of the cyanobacterial circadian genes, it was hypothesized that kaiA originated about 1000 Mya after two other key circadian genes, kaiB and kaiC¹⁰. This hypothesis was later revisited based on the growing available genomic data and much earlier origin of the kaiA gene was suggested^23,24. This revision is further supported by the results of the present study.

All kaiA genes can be divided into two large groups according to their domain architecture: single-domain and double-domain, respectively. The occurrence of these two versions of the gene is taxon-specific (Figs. 3 and S2). The sdkaiA occurs exclusively in Chroococcidiopsidales and Nostocales, while ddkaiA was found across all other cyanobacterial taxa. However, the N-terminal domain in ddkaiA varies quite significantly (especially as compared to the kaiA domain) across cyanobacteria and its homology to OmpR is quite weak. This suggests that the ancestral OmpR domain has been under weak selective constraints in the course of evolution that might result in its functional modification or even loss of the original function.

The KaiA domain of the protein is a key player in its binding to KaiC: several functionally important or critical residues have been identified experimentally in this domain^14,19. However, there are several more highly conserved or invariable residues identified in the present study (Table 1), which are apparently functionally important, but their exact function has yet to be determined.

There are several factors, which likely confer evolutionary constraints to the kaiA genes and limit HGTs even between the clades with the same domain architecture. In particular, this may be related to possible interaction with other elements of the circadian system. For example, some studies showed that KaiA competes with CikA in binding to KaiB and phosphorylation of KaiC²⁵. However, this mechanism is likely not universal, because bona fide CikA is absent in many cyanobacteria^11,22. Therefore, the observed variation in the kaiA domain and, respectively, above mentioned constraints may be related to functional modifications of KaiA to adjust to the circadian input pathway alterations. Wood et al.²⁶ reported that KaiA of S. elongatus PCC7942 binds the quinone by its N-terminal domain (OmpR, Fig. 1). This interaction helps to stabilize KaiA and is important for the mechanism of the KaiC phosphorylation. However, the sdKaiA proteins either lack the N-terminal domain completely or have it truncated (Fig. 1e–g) that means the circadian system in Chroococcidiopsidales and Nostocales should either lack this binding ability completely or have a different one. Furthermore, some cyanobacterial lineages have different N-terminal domains (Fig. 1) that assumes the different (if any) interaction with the quinone.

There is ample evidence that the cyanobacterial circadian system has experienced extensive evolutionary diversification (see, e.g.^11,24 for review). The results of the present study provide further support for that. Not only did the functional divergence occur between the single-domain and double-domain KaiA proteins, but also it occurred between the clades within these two subfamilies (data not shown).

In its native state, KaiA is a dimer whose only known function is binding to KaiC CII domain and inducing its autophosphorylation^27,28. Therefore, in the circadian system missing KaiA, the timing mechanism may be simplified as it was suggested for Prochlorococcus²⁹. However, it seems that even within the Prochlorococcus lineage, different versions of the simpler circadian system may exist. Indeed, as the results of the present study suggest, some Prochlorococcus strains possess, albeit truncated, but a highly conserved homolog of kaiA (Fig. 1). This extreme conservation, particularly at the functionally important residues common for the KaiA homologs across cyanobacteria, may suggest that the function of this truncated KaiA is somewhat similar to that of the bona fide protein. Strains of Prochlorococcus are known for their niche-specific adaptation, particularly with respect to the different light and temperature regimes, and extensive diversification into many co-existing ecotypes³⁰. The presence/absence of the kaiA homolog or its orphan replacement may be associated with this adaptation. For example, strains MIT9303 and MIT9313, which possess the orphan gene, were reported as adapted to low light³⁰. Importantly, despite the quite significant type I functional divergence (altered evolutionary rate), no type II divergence (radical amino acid changes) was detected in the KaiA domain of the truncated homologs. In these terms, it would be interesting to determine the exact functional significance of the universally conserved residues identified in the present study (Table 1).

The origin of the kaiA gene was initially estimated about 1000 Mya based on then available genomic data¹⁰. Since then, as more data has been accumulated, this estimate has been reconsidered^23,24. The results of the present study suggest that the kaiA gene is evolutionarily much older than it was thought before and its origin can be dated back to that of most cyanobacteria, i.e., about 3000 ± 500 Mya depending on the estimation methods.

After that, about 50–100 Mya, the kaiA gene was laterally transferred from the Synechococcus lineage to some Prochlorococcales and underwent a drastic truncation (Fig. 1e, Table 3). One more scenario may be based on the fact that the truncated kaiA homologs are apparently common in various Synechococcales and Nostocales and therefore the truncation might occur prior to the HGT to Prochlorococcales. These HGT and follow-up truncation (if any) might be related to the Cretaceous–Paleogene (K–Pg) extinction, which occurred about 66 MYA due to the asteroid impact having caused global ecological devastation, including rapid acidification of the oceans and light regime change^34,35.

There were several major structural changes in the kaiA genes (Table 3). The origin of sdkaiA and Chroococcidiopsidales falls within the Calymmian Period, the first geologic period in the Mesoproterozoic Era about 1500 MYA. These events might be associated with oxygenation of the Metaproterozoic ocean that occurred about 1570–1600 Mya³⁶. The domain fusion in kaiA of Phormidium occurred about 500–700 Mya, which corresponds to either the Ediacaran Period known for its Avalon explosion³⁷ or the Cambrian explosion³⁸.

Of course, the above interpretation of the obtained estimates has some limitations, one of which is the uncertainty of the fossil calibrations. On the other hand, the dates of the multiple events in the evolution of the kaiA genes inferred by the molecular methods match well the specific events in the Earth geochronology, which indeed might affect this evolution.

The sequences of the KaiA proteins and respective genes were retrieved from the GenBank using the KaiA sequence of Synechococcus elongatus PCC7942 (WP_011377921↗) as a query. We utilized the genomic BLASTP³⁹ to search the database. Only the sequences from the fully sequenced cyanobacterial genomes were used for the analyses. Bit score of 100 was applied as a cutoff value for sequence selection. Finally, the sequences from 226 strains were retained for the analysis. The used sequences are listed in Supplementary Table S1.

Besides, we used the 16S and 23S rRNA genes for the construction of the species tree. The respective DNA sequences of Acaryochloris marina strain MBIC11017 (CP000828↗) and Nostoc sp. PCC 7107 (CP003548↗) were used as the probes. In addition to the rRNA genes of cyanobacteria, the respective sequences of Staphylococcus aureus, Dehalococcoides mccartyi, Mycobacterium tuberculosis, and Candidatus Melainabacteria bacterium MEL.A1 were retrieved for the phylogenetic analysis (Table S1). In total 231 sequences were used in the analyses.

The full protein sequences were aligned using the combined sequence and structure-based algorithm implemented in the PRALINE server^40,41; the nucleotide sequences were aligned according to the protein alignment by Rev-Trans v.1.4 (http://www.cbs.dtu.dk/services/RevTrans/↗)⁴². The rRNA sequences were aligned using MAFFT⁴³. The aligned sequences were inspected visually and trimmed manually to remove poorly aligned regions and thus to improve a phylogenetic signal. The resulting final alignment of the KaiA protein subfamilies included 296 positions; the concatenated 16S-23S rRNA alignment counted 2941 positions.

The ConSurf server (http://consurf.tau.ac.il/↗) was utilized to identify group-specific conserved sites in the KaiA proteins⁴⁴. The analysis was conducted using a Bayesian procedure, the JTT substitution matrix, and Synechococcus elongatus KaiA (SMTL ID: 4G86_A) as a template⁴⁵.

The d_N values of the kaiA genes were calculated using the modified Nei-Gojobori method (with Jukes-Cantor correction and 1000 bootstrap replicates)⁴⁶ as implemented in MEGA X⁴⁷. To test the saturation of synonymous substitutions, pairwise d_S estimates were calculated first. Most pairwise d_S values were above 2, thus indicating that synonymous nucleotide substitutions were saturated. Also, the nucleotide diversity of the KaiA was analyzed using DnaSP v. 6.12.03⁴⁸. The level of variation was estimated by π⁴⁹.

Positive selection in the kaiA genes was analyzed using several approaches implemented in the Datamonkey server⁵⁰. Site-specific positive selection was analyzed using FUBAR⁵¹; the branch-site positive selection was tested using aBSREL⁵². A gene-wide test for positive selection was conducted using BUSTED⁵³.

The functional divergence between the KaiA subfamilies at the namesake domain was analyzed using the DIVERGE3 software⁵⁴. The following parameters were estimated: type I and type II functional divergence^55,56, effective number of sites related to this divergence. The False Discovery Rate (FDR) of the probability cut-off for the predicted sites was set at < 0.05.

Using only the KaiA domain for the phylogenetic inference yielded a poorly resolved tree. Therefore, the full KaiA protein alignment of 296 positions was utilized. The maximum-likelihood phylogenetic analysis was conducted using the IQ-TREE software⁵⁷ with the built-in ModelFinder function⁵⁸. Based on the ModelFinder analysis results, the JTT model⁵⁹ with a gamma distribution (α = 0.840) was used for the phylogenetic analysis of the KaiA homologs; the GTR model with a proportion of invariable sites and gamma distribution (GTR + I + 4G, p-inv = 0.106, α = 0.662) was applied to the analysis of the rRNA genes. The node support was inferred according to the ultrafast bootstrap⁶⁰, SH-aLRT branch test⁶¹, and approximate Bayes test⁶².

The Bayesian relaxed clock as implemented in BEAST v.2.6.2⁶³ was used to construct phylogenetic trees. The length of the MCMC chain was set for 100 million with trees sampling every 1,000 steps. The maximum clade credibility tree was determined using TreeAnnotator v.1.7.5 from the BEAST software package.

The horizontal gene transfers were determined using the bipartition dissimilarity algorithm implemented in the HGT-Detection software⁶⁴.

Two internal calibration points (CP1 & CP2) based on cyanobacteria fossil evidence were used for evolutionary time estimates. CP1 indicated the origins of Nostocales (1480–1300 Mya)⁶⁵, CP2 corresponded to the lower boundary of the estimates for the origin of cyanobacteria and was limited to the mid-Archean, before the Great Oxidation Event (~ 3000 Mya)⁶⁶. The height of the whole tree was constrained to 4000 Mya. The computations were conducted using BEAST v.2.6.2⁶⁷ and IQ-TREE⁵⁷ as mentioned above.

The predicted 3D models of KaiA proteins with the different domain architecture were constructed and refined using the respective methods implemented in the GalaxyWEB server⁶⁸. The quality of the models was assessed by the structure assessment tool of the SWISS-MODEL server⁶⁹.

Supplementary Information. Supplementary Table S1.